This one was a pain to grind out because there's really no way to know where you are in the process.
I played the game through about 4 times (for other achievements). In my fourth play-through, when I got to Mephisto's Realm, I used Dr. Strange and told myself, "Well, since I'm here, I'll just find a good spot and use the levitate method posted on TA." I did just that and I even counted the guys I threw off. I stopped counting around 550. Something was definitely wrong and I was a little annoyed that I just wasted about an hour.
So I finished up the game, got all the other achievements I needed (Sims, outfits, etc) and decided I was going to go for this one again. I used Taku's suggested method involving Invisible Woman and her levitate ability. I went to an Asgard sim mission, got to the bridge and got to work. I had Dr. Strange active also so many of the bad guys were concentrating on beating him up while I just grabbed them one at a time from a distance.
Long story short, after a little over 100 levitates, the darn thing popped. I was pretty happy about that.
So the achievement MUST carry over for each playthrough. However, the bunch I did with Dr. Strange earlier must have either glitched a lot or not counted somehow. Maybe it was the spot I was in. Maybe it was something with the saved games. There's just no way to know.
So I have no idea how to really advise anyone to get this, but if I had to go back in time, I would probably go for this one early, before even completing the game. I'd use one of the Asgard Sim missions and whatever character I wanted. Then I'd start throwing dudes and keeping track of when the other achievements popped that might give clues. There's one for throwing 50 off a ledge or killing 100 enemies, etc. At least you'll have some idea of where you are.
Good luck. Hopefully this experience will help you a little.
Now if they'd just release a GOLD version of Ultimate Alliance 2 with the DLC on it that I missed! Ugh!